In order to observe the southern stars that could not be seen on the observatory’s latitude, the scientists organized 2 affiliates. One of them was an astrophysical station in the Crimean town of Simeiz (Simeiz Observatory), which had been organized on the basis of a private observatory presented to the Pulkovo Observatory by an astronomy lover N.S.Maltsev in 1908. The other affiliate of the Pulkovo Observatory was an astrometric station in Nikolaev – a former observatory of the Department of the Navy, (today’s Nikolaev Astronomical Observatory).

The observatory staff was very badly affected by the Great Purge and many Pulkovo astronomers, including the director Boris Gerasimovich, were arrested and executed in the late 1930s.[5]

During the siege of Leningrad (1941–1944), the Observatory became the target of fierce Germanair raids and artillerybombardment. All of the buildings were completely destroyed. Under dramatic circumstances, the main instruments were saved and stored safely in Leningrad, including the lens of the destroyed 30-inch refractor, and a significant part of the unique library with manuscripts and important works from the 15th to 19th century. On February 5, 1997, nearly 1,500 of the 3,852 books were destroyed by malicious arson and the rest of the library items were damaged by flames, smoke or water.[4][6]

Even before the end of the war, the Soviet government made a decision to restore the Observatory. In 1946, it began the construction after having cleared the territory. In May 1954, the Observatory was re-opened, not only having been restored but considerably expanded in terms of instruments, employees and research subjects. New departments had been created, such as the Department of Radio Astronomy and Department of Instrument Making (with its own optical and mechanical workshop). The surviving old instruments were repaired, modernized and put into service once again. Also installed were new instruments, such as the 26-inch (660 mm) refractor,[3] a horizontal meridian device, a photographic polar telescope, a big zenith telescope, stellar interferometer, 2 solar telescopes, coronagraph, a big radio telescope and all kinds of labware. The Simeiz station became a part of the new Crimean Astrophysical Observatory of the Soviet Academy of Sciences in 1945. They also built the Kislovodsk Mountain Astronomical Station and a laboratory in Blagoveshchensk. The observatory organized many expeditions for determining differences of longitudes, observing passages of Venus and solar eclipses, and studying astroclimate. In 1962, the Observatory sent an expedition to Chile to observe stars in the southern skies.[7] The 65 cm Zeiss telescope was originally intended as a gift from then Chancellor of Germany Adolf Hitler to the Italian Benito Mussolini, but it was not delivered and instead was taken by the Soviet Union.[8]

^Eremeeva, A. I. (November 1995), "Political Repression and Personality: The History of Political Repression Against Soviet Astronomers", Journal for the History of Astronomy: 297, Bibcode:1995JHA....26..297E